id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2421 'MDFF_Mgr' object has no attribute '_c_pointer' Tristan Croll Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.20.8-200.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine ChimeraX Version: 0.91 (2019-09-17) Description Looks like there has been an API change? I haven't made any changes to ISOLDE that could have caused this. MDFF_Mgr is modeled on the `Collections` molc API. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-09-17) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open xaituo_scoat_refine_4.pdb Summary of feedback from opening xaituo_scoat_refine_4.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-09-18 Time 20:04:40 CEST +0200 (1568829880.49 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /home/tic20/structure_dump/kaituo/AutoSol357_denmod.mtz 45 messages similar to the above omitted Chain information for xaituo_scoat_refine_4.pdb #1 --- Chain | Description A | No description available > isolde start > set selectionWidth 4 Missing or corrupted CRYST1 card found in the PDB file. This model will be treated as a cryo-EM model until associated with an MTZ file containing symmetry information. Chain information for xaituo_scoat_refine_4.pdb --- Chain | Description 1.3/A | No description available Done loading forcefield > addh Summary of feedback from adding hydrogens to xaituo_scoat_refine_4.pdb #1.3 --- notes | No usable SEQRES records for xaituo_scoat_refine_4.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 45 Chain-initial residues that are not actual N termini: /A GLY 118 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A PHE 676, /A ALA 116 558 hydrogen bonds Adding 'H' to /A GLY 118 /A PHE 676 is not terminus, removing H atom from 'C' /A ALA 116 is not terminus, removing H atom from 'C' 4738 hydrogens added (CLIPPER) NOTE: No symmetry information found in model. Using symmetry from MTZ file. > hide HC > close #1.1.1.5 > set bgColor white > select #1 9376 atoms, 9441 bonds, 11 pseudobonds, 27 models selected Bad residue number: 483 Doing nothing > addh metalDist 1 Summary of feedback from adding hydrogens to xaituo_scoat_refine_4.pdb #1.3 --- notes | No usable SEQRES records for xaituo_scoat_refine_4.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 45 Chain-initial residues that are not actual N termini: /A GLY 118 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A PHE 676, /A ALA 116 541 hydrogen bonds /A PHE 676 is not terminus, removing H atom from 'C' /A ALA 116 is not terminus, removing H atom from 'C' 1 hydrogens added > select #1 9377 atoms, 9442 bonds, 11 pseudobonds, 32 models selected > toolshed show Shell /opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > color sel bychain > color sel byhetero > select clear > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2097, in _backrub_rotamer self._apply_backrub(None, None) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. > select down 2 atoms, 1 bond, 1 model selected > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2107, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 409, in apply_backrub map_weight = mdff_mgr.global_k File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' Error processing trigger ""sim paused"": AttributeError: 'MDFF_Mgr' object has no attribute '_c_pointer' File ""/home/tic20/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 1800, in _get_global_k return f(self._c_pointer) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 410.93 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party nonchimerax Eric Pettersen Tom Goddard all ChimeraX